Summon Nights 1&2 a cult classic GBA game the second one came out not too long ago, they're great, you get to choose your story with almost trivial questions so its almost never the same on different playthroughs.
Megaman battle network 2 (best one in the series)
" " " " " "" " " " " " " " " " 3 (sequel, pretty good too)
Final Fantasy 1+2
Golden Sun
Final Fantasy Tactics Advanced.
